Contacts of the helix formed by residues 195 - 213 (chain 7) in PDB entry 3J7Y
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 195 (chain 7).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1937 MET 4.7 5.2 - - - +
1947 PRO* 1.3 77.0 - - - +
1967 LYS* 1.3 63.6 + - - +
1977 GLU* 3.3 12.8 + - - +
1987 ASN* 3.2 27.3 + - - +
1997 LEU* 3.2 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1957 THR* 1.3 71.5 - - - +
1977 GLU* 1.3 61.5 + - + +
1997 LEU* 3.2 16.5 + - + +
2007 ARG* 2.9 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1957 THR* 3.2 11.3 + - - +
1967 LYS* 1.3 78.2 - - + +
1987 ASN* 1.3 59.9 + - - +
2007 ARG* 3.2 15.6 + - - +
2017 SER* 2.9 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 198 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1587 PHE* 6.2 2.0 - - - -
1937 MET 4.4 4.2 + - - -
1947 PRO* 3.6 26.8 - - + +
1957 THR* 3.2 28.2 + - - +
1967 LYS 3.2 0.4 - - - -
1977 GLU* 1.3 78.2 - - - +
1997 LEU* 1.3 58.5 + - - +
2017 SER* 2.5 26.3 + - - +
2027 PHE* 2.9 28.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1947 PRO* 5.2 8.5 - - + +
1957 THR 3.2 14.8 + - - +
1967 LYS* 3.2 19.9 + - + +
1987 ASN* 1.3 79.9 - - - +
2007 ARG* 1.3 57.2 + - + +
2027 PHE* 3.2 9.3 + - + +
2037 THR* 2.9 34.9 + - + +
2807 VAL* 3.7 32.3 - - + +
2817 SER 3.3 21.5 - - - +
2827 ALA* 4.0 15.9 - - + +
2837 VAL* 4.4 15.0 - - + -
2977 PHE* 5.8 0.4 - - + -
3217 ARG* 6.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 200 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967 LYS* 2.9 25.3 + - + +
1977 GLU* 3.4 15.3 - - - +
1997 LEU* 1.3 77.1 - - + +
2017 SER* 1.3 56.9 + - - +
2037 THR* 2.3 29.6 + - + +
2047 LYS* 2.9 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1977 GLU 2.9 12.6 + - - -
1987 ASN* 2.5 26.1 + - - -
2007 ARG* 1.3 75.5 - - - +
2027 PHE* 1.3 64.3 + - - +
2047 LYS* 3.2 14.1 + - - +
2057 ASP* 2.9 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1507 MET* 4.9 1.8 - - + -
1537 VAL* 3.4 24.0 - - + +
1547 ILE* 3.6 30.7 - - + -
1577 ALA* 3.7 26.7 - - + -
1587 PHE* 3.9 23.3 - + - -
1947 PRO* 6.2 2.5 - - + -
1987 ASN* 2.9 31.9 + - + +
1997 LEU* 3.2 13.2 + - + +
2017 SER* 1.3 86.7 + - - +
2037 THR* 1.3 63.6 + - - +
2057 ASP* 3.2 7.3 + - - +
2067 ALA* 3.0 21.3 + - - +
2807 VAL* 4.2 20.6 - - + -
2977 PHE* 3.6 22.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1997 LEU* 2.9 21.4 + - + +
2007 ARG* 2.3 32.2 + - + +
2027 PHE* 1.3 75.7 - - - +
2047 LYS* 1.3 61.8 + - - +
2067 ALA* 3.2 6.4 + - - +
2077 HIS* 2.9 43.4 + - - -
2787 TYR 4.6 4.0 - - - -
2797 GLU* 4.0 13.2 - - + +
2807 VAL* 3.5 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007 ARG* 2.9 16.9 + - + +
2017 SER* 3.3 15.0 - - - +
2037 THR* 1.3 83.0 + - - +
2057 ASP* 1.3 58.8 + - - +
2077 HIS* 3.2 10.2 + - - +
2087 ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 205 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1537 VAL* 3.8 18.2 - - + +
1567 ARG* 5.7 1.2 - - - +
1577 ALA* 4.1 26.3 + - - +
2017 SER* 2.9 24.1 + - - +
2027 PHE* 3.3 8.2 - - - +
2047 LYS* 1.3 78.0 - - - +
2067 ALA* 1.3 57.7 + - - +
2087 ALA* 3.2 9.6 + - - +
2097 LEU* 2.9 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 MET* 5.0 2.7 - - + +
1537 VAL* 3.6 17.4 - - + +
2027 PHE 3.0 12.3 + - - +
2037 THR* 3.4 10.3 - - - +
2057 ASP* 1.3 75.9 - - - +
2077 HIS* 1.3 56.8 + - - +
2097 LEU* 3.2 7.2 + - - +
2107 ILE* 2.9 34.8 + - - +
2787 TYR* 3.3 39.9 - - + -
2807 VAL* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 207 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2037 THR* 2.9 30.4 + - - -
2047 LYS* 3.2 11.2 + - + +
2067 ALA* 1.3 76.7 - - - +
2087 ALA* 1.3 56.4 + - - +
2107 ILE* 3.2 14.4 + - + +
2117 TYR* 2.9 28.8 + - - +
2767 PHE 3.8 22.4 + - - -
2777 GLN* 4.8 1.6 - - - -
2787 TYR* 3.0 32.8 + - + -
2797 GLU* 5.0 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2047 LYS 2.9 12.3 + - - +
2057 ASP* 3.3 12.3 - - - +
2077 HIS* 1.3 75.6 - - - +
2097 LEU* 1.3 57.6 + - + +
2117 TYR* 3.2 10.6 + - - +
2127 LYS* 2.9 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 MET* 4.2 16.8 - - + +
1527 CYS* 3.9 29.6 - - + -
1537 VAL* 3.5 32.3 - - + +
1567 ARG* 5.8 6.1 - - - +
2057 ASP* 2.9 14.5 + - + +
2067 ALA* 3.3 8.3 - - - +
2087 ALA* 1.3 76.3 - - - +
2107 ILE* 1.3 63.0 - - + +
2127 LYS* 3.2 35.4 + - + +
2137 ASP 3.2 9.4 + - - -
2147 LEU* 4.6 16.8 - - + +
2577 ILE* 5.8 2.9 - - + -
2727 THR* 3.4 9.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 MET* 3.7 17.5 - - + -
2067 ALA 2.9 22.1 + - - +
2077 HIS* 3.2 18.8 + - + +
2097 LEU* 1.3 75.5 - - - +
2117 TYR* 1.3 66.2 + - - +
2137 ASP* 3.1 18.0 + - - +
2727 THR* 3.4 25.1 + - - +
2737 SER* 3.9 11.4 + - - +
2757 CYS* 3.3 33.4 - - + +
2767 PHE* 5.0 2.5 - - - +
2787 TYR* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 211 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2077 HIS 2.9 12.4 + - - +
2087 ALA* 3.2 14.1 + - - +
2107 ILE* 1.3 80.8 - - - +
2127 LYS* 1.3 71.2 + - + +
2137 ASP* 3.2 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2087 ALA* 2.9 24.7 + - - +
2097 LEU* 3.2 29.8 + - + +
2117 TYR* 1.3 82.8 - - + +
2137 ASP* 1.3 68.4 + - - +
2147 LEU* 4.1 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2097 LEU 3.2 5.1 + - - -
2107 ILE 3.1 9.2 + - - +
2117 TYR 3.5 9.9 - - - +
2127 LYS* 1.3 81.1 - - - +
2147 LEU* 1.3 58.6 + - - +
2157 PRO* 4.2 1.4 - - - +
2717 ARG* 2.8 53.4 + - - +
2727 THR* 3.3 8.5 - - - -
2737 SER* 3.2 30.3 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il